I am working on protein sequences to find best feature for SVM. So i was right now try to work on pssm matrix feature for protein sequence. If i apply psi-blast with "nr" data base on my protein sequences it gives pssm matrix as an output.But my problem is i have 2000 protein sequences at a time i am able to find only one sequences pssm matrix out of 2000. So what can i do for to find all 2000 sequences pssm matrix. If any one have any idea please send the post and try to give the answer. Thank to all in advance.